Picky nascent peptides do not talk to foreign ribosomes.

O ne of the least understood aspects of protein synthesis is communication between the ribosome and the nascent peptide. Chiba et al. (1) in this issue of PNAS reveal that, at least in some cases, these dialogues can be species-specific. The ribosome assembles amino acids into proteins in the peptidyl transferase center (PTC) located at the interface side of the large ribosomal subunit. On its way out, the nascent peptide passes through the exit tunnel. This ∼100-Å-long and 10to 20-Å-wide irregularly shaped vent spans the entire body of the subunit. The tunnel is not just a hole but rather a functionally important compartment where the structure of the nascent peptide is monitored and from which specific peptides can signal the ribosome to slow down its rate of elongation or even completely stop translation. The bestcharacterized manifestation of this feedback mechanism is nascent peptidedependent ribosome stalling when the PTC becomes incapacitated after having polymerized the effector (stalling) domain of the regulatory nascent peptide. Such programmed translation arrest is sensitive to the cellular environment and therefore, can be used for control of gene expression. A number of genes regulated on the basis of nascent peptide recognition have been identified in bacteria and eukaryotes (2). Despite the generally conserved nature of the ribosome, the fine structure of the exit tunnel exhibits considerable variations. Nearly 20% of rRNA nucleotides forming the exit tunnel differ between Gram-negative and Gram-positive bacteria (Fig. 1B). The variation in tunnel properties can be further influenced by the idiosyncratic posttranscriptional rRNA modifications and the divergence of tunnel proteins. These differences may affect the overall shape of the tunnel (Fig. 1C) as well as its chemical characteristics (polarity, pattern of hydrogen donors and acceptors, electrostatics, etc.) (3, 4), and thus, they may alter functional interactions of the ribosome with the protein being synthesized. Significant progress has been achieved in recent years in elucidating the mechanism of translation modulation by the nascent peptide. Sequences critical for stalling have been characterized for several regulatory peptides (5–8), a number of rRNA and protein residues at the walls of the exit tunnel that are involved in nascent peptide recognition and triggering of the ribosomal response have been mapped (6, 7, 9), and cryo-EM structures of stalled ribosome complexes are starting to emerge (10, 11). Nevertheless, very little is still known about the principles of nascent peptide–ribosome communication. Chiba et al. (1) illuminate an important aspect of the operation of this mechanism: the specificity of the ribosome to recognition of the stalling peptide. Chiba et al. (1) examine programmed translation arrest induced by the regulatory proteins SecM and MifM found in Escherichia coli and Bacillus subtilis, respectively. In Gram-negative E. coli, nascent peptide-dependent ribosome stalling at the secM ORF activates translation of the downstream gene-encoding protein export chaperon SecA (7). Translation arrest at the mifM ORF in Gram-positive B. subtilis leads to activation of expression of an alternative membrane biogenesis factor YidC2 (12). Although SecM and MifM peptides elicit the same ribosomal response—programmed translation Fig. 1. The variation in the ribosome tunnel structure between species may affect nascent peptide recognition. (A) The SecM and MifM stalling peptides arrest progression of only cognate ribosomes. (B) The tunnel nucleotide residues differing between Gram-negative E. coli and Gram-positive B. subtilis are shown by red arrowheads. Segments of the large ribosomal subunit rRNA that form the walls of the exit tunnel are indicated by thick lines (20). (C) Difference in the shape of the exit tunnels in ribosomes of Gram-negative (E. coli; green) and Gram-positive (Deinococcus radiodurans; orange) bacteria. The tunnel shape from the structures of the respective large ribosomal subunits was extracted as described in ref. 4.